If I were to try to explain the origin of theism as naturalistically as possible, my starting point would not be trying to explain causes of natural phenomena (which D'Souza points out, is an anachronistic reading of history) but look at something like the communion of the saints as natural to human society. And that communion, as a community, has a leader: the Holy One. This theme is not utterly independent of seeking causes of nature. But an adequate explanation must include both. By "natural" I don't mean "non-supernatural," for nature itself points to God. Especially human nature: if there is freedom, then there is more to nature than an ontological-naturalist (as in anti-supernatralist) is willing to recognize; and there is more to nature than a methodological-naturalist (that is, one who as a matter of principle, when doing science admits only of materialistic explanations) is able to recognize.
Commentary and discussion regarding science, faith and culture by Leo White